The Trump administration returned to the Supreme Court on Tuesday in the case of eight men it seeks to deport to South Sudan, asking the justices to make clear that an order they issued on Monday was intended to apply to the group.

The clarity was apparently needed because the Supreme Court on Monday had issued only a brief order letting the government send migrants to countries with which they have no connection without giving them a chance to argue they would face torture. The court provided no explanation of its reasoning.

The Supreme Court’s order paused an injunction issued by Judge Brian E. Murphy, of the U.S. District Court in Boston, who had forbidden the deportations of all migrants to third countries unless they were afforded due process.

Soon after the Supreme Court ruled, lawyers for the men filed an emergency motion with Judge Murphy asking him to continue blocking the deportations of eight men currently held in Djibouti.

In a brief order Monday night, the judge denied the motion as unnecessary. He said that he had issued a separate ruling last month, different from the one the Supreme Court had paused, protecting the men in Djibouti from immediate removal.

That left the fate of the men unclear, as President Trump and a top aide cried foul.

Judge Murphy “knew absolutely nothing about the situation” and was “absolutely out of control,” Mr. Trump wrote on social media.